annotate nhmmer.xml @ 7:b28e8ed99424 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 0bccf5220ed6549db7e053f85bbe917326b0a0be"
author iuc
date Wed, 21 Jul 2021 14:11:12 +0000
parents 314b778b8ffa
children
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1 <?xml version="1.0"?>
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2 <tool id="hmmer_nhmmer" name="nhmmer" version="@TOOL_VERSION@+galaxy0">
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3 <description>search a DNA model or alignment against a DNA database (BLASTN-like)</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <expand macro="stdio"/>
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9 <command><![CDATA[
6
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10 @ADDTHREADS@
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11 nhmmer
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12
5
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13 @OFORMAT_WITH_OPTS@
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14 @HSSI@
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15 @THRESHOLDS_NODOM@
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16 @CUT@
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17 @ACCEL_HEUR@
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18 @FORMAT_SELECTOR@
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19 @ADV_OPTS@
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20 @LENGTHS@
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21 @CPU@
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22 @SEED@
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23
3
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24 '$hmmfile'
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25 '$seqfile'
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26 > '$output'
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27 ]]></command>
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28 <inputs>
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29 <expand macro="input_hmm" />
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30 <param name="seqfile" type="data" format="fasta" label="Target sequence file"/>
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31 <expand macro="oformat_with_opts_dfam_alisc"/>
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32 <expand macro="hssi"/>
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33 <expand macro="thresholds_nodom"/>
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34 <expand macro="cut" />
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35 <expand macro="accel_heur_xml"/>
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36 <expand macro="format_selector_noprot"/>
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37 <expand macro="adv_opts"/>
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38 <expand macro="lengths"/>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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39 <!-- TODO: block_length toponly bottomonly -->
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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40 <expand macro="seed"/>
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41 </inputs>
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42 <outputs>
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43 <expand macro="output_dfam_alisc" tool="NHMMER"/>
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44 </outputs>
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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45 <tests>
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46 <test expect_num_outputs="4">
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47 <param name="hmmfile" value="MADE1.hmm"/>
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48 <param name="seqfile" value="dna_target.fa"/>
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49 <expand macro="oformat_test" />
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50 <param name="oformat" value="tblout,dfamtblout,aliscoresout"/>
0
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51 <expand macro="seed_test" />
5
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52 <output name="output" file="nhmmer.out" lines_diff="16">
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53 <expand macro="assert_out" tool="nhmmer"/>
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54 </output>
b4fe2f703b4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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55 <output name="tblout" file="nhmmer.out.tblout" lines_diff="12">
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56 <expand macro="assert_tblout" tool="nhmmer"/>
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57 </output>
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58 <output name="aliscoresout" file="nhmmer.out.aliscoresout" lines_diff="10"/>
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59 <output name="dfamtblout" file="nhmmer.out.dfamtblout" lines_diff="10">
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60 <assert_contents>
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61 <has_line_matching expression="# hit scores"/>
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62 </assert_contents>
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63 </output>
b4fe2f703b4b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 7d31599a80c15f11ed00b2b3cbfb77ed6dfc8f3d"
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64 </test>
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65 <test expect_num_outputs="1">
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66 <param name="hmmfile" value="MADE1.hmm"/>
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67 <param name="seqfile" value="dna_target.fa"/>
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68 <expand macro="oformat_test" />
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69 <param name="oformat" value=""/>
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70 <expand macro="seed_test" />
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71 <output name="output" file="nhmmer.out" lines_diff="16">
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72 <expand macro="assert_out" tool="nhmmer"/>
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73 </output>
0
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74 </test>
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75 </tests>
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76 <help><![CDATA[
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77 @HELP_PRE@
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78
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79 nhmmer is used to search one or more nucleotide queries against a nucleotide
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80 sequence database. For each query in <queryfile>, use that query to search the
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81 target database of sequences in <seqdb>, and output a ranked list of the hits
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82 with the most significant matches to the query. A query may be either a profile
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83 model built using hmmbuild, a sequence alignment, or a single sequence.
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84 Sequence based queries can be in a number of formats (see --qformat), and can
f239ab5f45f4 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit 4261b86af790a3535c0b9a8122f92225f8f67b47
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85 typically be autodetected. Note that only Stockholm format supports the use of
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86 multiple sequence-based queries.
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87
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88 @HELP_PRE_OTH@
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89
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90 @OFORMAT_WITH_OPTS_N_HELP@
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91 @HSSI_HELP@
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92 @THRESHOLDS_NODOM_HELP@
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93 @CUT_HELP@
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94 @ACCEL_HEUR_HELP@
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95 @FORMAT_SELECTOR_HELP@
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96 @ADV_OPTS_HELP@
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97 @LENGTHS_HELP@
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98 @SEED_HELP@
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99
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100 @ATTRIBUTION@
3
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101 ]]></help>
0
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102 <expand macro="citation"/>
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103 </tool>